On the morning of Wednesday, 15 October 1586, Mary Queen of Scots entered the crowded courtroom at Fotheringhay Castle, charged with treason. She had been accused of plotting to assassinate Elizabeth I, in order to take the English crown for herself. Sir Francis Walsingham, Elizabeth's Principal Secretary, had already arrested the other suspects, extracted confessions, and executed them. Now he planned to prove that Mary was at the heart of the plot, and was therefore equally culpable and equally deserving of death.

The conspirators were a group of young English Catholic noblemen, intent on removing Elizabeth, a Protestant, and replacing her with Mary, a fellow Catholic. It was apparent to the court that Mary was a figurehead for the conspirators, but it was not clear that she had actually given them her blessing. In fact, Mary had indeed authorised the plot. The challenge for Walsingham was to prove the link between Mary and the plotters.

Crucially Walsingham had managed to obtain the letters sent between Mary and the plotters. However, Mary had been careful to ensure that all her correspondence with the conspirators had been written in a cipher known as the substitution cipher. The cipher turned her words into a series of symbols, so that even if the letters came into Walsingham's possession, Mary hoped that he wouldn't be able to understand them or use them as evidence.

Not for the first time, a life hung on the strength of a cipher.